.TH g_energy 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5"
.SH NAME
g_energy - writes energies to xvg files and displays averages

.B VERSION 4.5
.SH SYNOPSIS
\f3g_energy\fP
.BI "\-f" " ener.edr "
.BI "\-f2" " ener.edr "
.BI "\-s" " topol.tpr "
.BI "\-o" " energy.xvg "
.BI "\-viol" " violaver.xvg "
.BI "\-pairs" " pairs.xvg "
.BI "\-ora" " orienta.xvg "
.BI "\-ort" " orientt.xvg "
.BI "\-oda" " orideva.xvg "
.BI "\-odr" " oridevr.xvg "
.BI "\-odt" " oridevt.xvg "
.BI "\-oten" " oriten.xvg "
.BI "\-corr" " enecorr.xvg "
.BI "\-vis" " visco.xvg "
.BI "\-ravg" " runavgdf.xvg "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-b" " time "
.BI "\-e" " time "
.BI "\-[no]w" ""
.BI "\-xvg" " enum "
.BI "\-[no]fee" ""
.BI "\-fetemp" " real "
.BI "\-zero" " real "
.BI "\-[no]sum" ""
.BI "\-[no]dp" ""
.BI "\-nbmin" " int "
.BI "\-nbmax" " int "
.BI "\-[no]mutot" ""
.BI "\-skip" " int "
.BI "\-[no]aver" ""
.BI "\-nmol" " int "
.BI "\-nconstr" " int "
.BI "\-[no]fluc" ""
.BI "\-[no]orinst" ""
.BI "\-[no]ovec" ""
.BI "\-acflen" " int "
.BI "\-[no]normalize" ""
.BI "\-P" " enum "
.BI "\-fitfn" " enum "
.BI "\-ncskip" " int "
.BI "\-beginfit" " real "
.BI "\-endfit" " real "
.SH DESCRIPTION
\&g_energy extracts energy components or distance restraint
\&data from an energy file. The user is prompted to interactively
\&select the energy terms she wants.


\&Average, RMSD and drift are calculated with full precision from the
\&simulation (see printed manual). Drift is calculated by performing
\&a LSQ fit of the data to a straight line. The reported total drift
\&is the difference of the fit at the first and last point.
\&An error estimate of the average is given based on a block averages
\&over 5 blocks using the full precision averages. The error estimate
\&can be performed over multiple block lengths with the options
\&\fB \-nbmin\fR and \fB \-nbmax\fR.
\&Note that in most cases the energy files contains averages over all
\&MD steps, or over many more points than the number of frames in
\&energy file. This makes the g_energy statistics output more accurate
\&than the xvg output. When exact averages are not present in the energy
\&file the statistics mentioned above is simply over the single, per\-frame
\&energy values.


\&The term fluctuation gives the RMSD around the LSQ fit.


\&Some fluctuation\-dependent properties can be calculated provided
\&the correct energy terms are selected. The following properties
\&will be computed:

\&Property                        Energy terms needed

\&\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-

\&Heat capacity Cp (NPT sims):    Enthalpy, Temp     

\&Heat capacity Cv (NVT sims):    Etot, Temp         

\&Thermal expansion coeff. (NPT): Enthalpy, Vol, Temp

\&Isothermal compressibility:     Vol, Temp          

\&Adiabatic bulk modulus:         Vol, Temp          

\&\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-

\&You always need to set the number of molecules \fB \-nmol\fR, and,
\&if you used constraints in your simulations you will need to give
\&the number of constraints per molecule \fB \-nconstr\fR in order to
\&correct for this: (nconstr/2) kB is subtracted from the heat
\&capacity in this case. For instance in the case of rigid water
\&you need to give the value 3 to this option.


\&When the \fB \-viol\fR option is set, the time averaged
\&violations are plotted and the running time\-averaged and
\&instantaneous sum of violations are recalculated. Additionally
\&running time\-averaged and instantaneous distances between
\&selected pairs can be plotted with the \fB \-pairs\fR option.


\&Options \fB \-ora\fR, \fB \-ort\fR, \fB \-oda\fR, \fB \-odr\fR and
\&\fB \-odt\fR are used for analyzing orientation restraint data.
\&The first two options plot the orientation, the last three the
\&deviations of the orientations from the experimental values.
\&The options that end on an 'a' plot the average over time
\&as a function of restraint. The options that end on a 't'
\&prompt the user for restraint label numbers and plot the data
\&as a function of time. Option \fB \-odr\fR plots the RMS
\&deviation as a function of restraint.
\&When the run used time or ensemble averaged orientation restraints,
\&option \fB \-orinst\fR can be used to analyse the instantaneous,
\&not ensemble\-averaged orientations and deviations instead of
\&the time and ensemble averages.


\&Option \fB \-oten\fR plots the eigenvalues of the molecular order
\&tensor for each orientation restraint experiment. With option
\&\fB \-ovec\fR also the eigenvectors are plotted.


\&With \fB \-fee\fR an estimate is calculated for the free\-energy
\&difference with an ideal gas state: 

\&  Delta A = A(N,V,T) \- A_idgas(N,V,T) = kT ln  e(Upot/kT) 

\&  Delta G = G(N,p,T) \- G_idgas(N,p,T) = kT ln  e(Upot/kT) 

\&where k is Boltzmann's constant, T is set by \fB \-fetemp\fR and
\&the average is over the ensemble (or time in a trajectory).
\&Note that this is in principle
\&only correct when averaging over the whole (Boltzmann) ensemble
\&and using the potential energy. This also allows for an entropy
\&estimate using:

\&  Delta S(N,V,T) = S(N,V,T) \- S_idgas(N,V,T) = (Upot \- Delta A)/T

\&  Delta S(N,p,T) = S(N,p,T) \- S_idgas(N,p,T) = (Upot + pV \- Delta G)/T
\&


\&When a second energy file is specified (\fB \-f2\fR), a free energy
\&difference is calculated dF = \-kT ln  e  \-(EB\-EA)/kT A ,
\&where EA and EB are the energies from the first and second energy
\&files, and the average is over the ensemble A. \fB NOTE\fR that
\&the energies must both be calculated from the same trajectory.
.SH FILES
.BI "\-f" " ener.edr" 
.B Input
 Energy file 

.BI "\-f2" " ener.edr" 
.B Input, Opt.
 Energy file 

.BI "\-s" " topol.tpr" 
.B Input, Opt.
 Run input file: tpr tpb tpa 

.BI "\-o" " energy.xvg" 
.B Output
 xvgr/xmgr file 

.BI "\-viol" " violaver.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-pairs" " pairs.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-ora" " orienta.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-ort" " orientt.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-oda" " orideva.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-odr" " oridevr.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-odt" " oridevt.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-oten" " oriten.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-corr" " enecorr.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-vis" " visco.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-ravg" " runavgdf.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 19" 
 Set the nicelevel

.BI "\-b"  " time" " 0     " 
 First frame (ps) to read from trajectory

.BI "\-e"  " time" " 0     " 
 Last frame (ps) to read from trajectory

.BI "\-[no]w"  "no    "
 View output xvg, xpm, eps and pdb files

.BI "\-xvg"  " enum" " xmgrace" 
 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR

.BI "\-[no]fee"  "no    "
 Do a free energy estimate

.BI "\-fetemp"  " real" " 300   " 
 Reference temperature for free energy calculation

.BI "\-zero"  " real" " 0     " 
 Subtract a zero\-point energy

.BI "\-[no]sum"  "no    "
 Sum the energy terms selected rather than display them all

.BI "\-[no]dp"  "no    "
 Print energies in high precision

.BI "\-nbmin"  " int" " 5" 
 Minimum number of blocks for error estimate

.BI "\-nbmax"  " int" " 5" 
 Maximum number of blocks for error estimate

.BI "\-[no]mutot"  "no    "
 Compute the total dipole moment from the components

.BI "\-skip"  " int" " 0" 
 Skip number of frames between data points

.BI "\-[no]aver"  "no    "
 Also print the exact average and rmsd stored in the energy frames (only when 1 term is requested)

.BI "\-nmol"  " int" " 1" 
 Number of molecules in your sample: the energies are divided by this number

.BI "\-nconstr"  " int" " 0" 
 Number of constraints per molecule. Necessary for calculating the heat capacity

.BI "\-[no]fluc"  "no    "
 Calculate autocorrelation of energy fluctuations rather than energy itself

.BI "\-[no]orinst"  "no    "
 Analyse instantaneous orientation data

.BI "\-[no]ovec"  "no    "
 Also plot the eigenvectors with \-oten

.BI "\-acflen"  " int" " \-1" 
 Length of the ACF, default is half the number of frames

.BI "\-[no]normalize"  "yes   "
 Normalize ACF

.BI "\-P"  " enum" " 0" 
 Order of Legendre polynomial for ACF (0 indicates none): \fB 0\fR, \fB 1\fR, \fB 2\fR or \fB 3\fR

.BI "\-fitfn"  " enum" " none" 
 Fit function: \fB none\fR, \fB exp\fR, \fB aexp\fR, \fB exp_exp\fR, \fB vac\fR, \fB exp5\fR, \fB exp7\fR or \fB exp9\fR

.BI "\-ncskip"  " int" " 0" 
 Skip N points in the output file of correlation functions

.BI "\-beginfit"  " real" " 0     " 
 Time where to begin the exponential fit of the correlation function

.BI "\-endfit"  " real" " \-1    " 
 Time where to end the exponential fit of the correlation function, \-1 is until the end

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.
